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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/ElementalAnalysis.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,192 @@ +<html> +<head> +<title>MayaChemTools:Documentation:ElementalAnalysis.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./DBTablesToTextFiles.html" title="DBTablesToTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ElementalAnalysisSDFiles.html" title="ElementalAnalysisSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>ElementalAnalysis.pl</strong></td><td width="33%" align="right"><a href="././code/ElementalAnalysis.html" title="View source code">Code</a> | <a href="./../pdf/ElementalAnalysis.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ElementalAnalysis.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ElementalAnalysis.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ElementalAnalysis.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>ElementalAnalysis.pl - Perform elemental analysis using specified formulas</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>ElementalAnalysis.pl Formula(s)...</p> +<p>ElementalAnalysis.pl [<strong>-h, --help</strong>] +[<strong>-m, --mode</strong> All | "ElementalAnalysis, [MolecularWeight, ExactMass]"] +[<strong>--outdelim</strong> comma | tab | semicolon] +[<strong>--output</strong> STDOUT | File] [<strong>--outputstyle</strong> FormulaBlock | FormulaRows] +[<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname] +[<strong>-v --valuelabels</strong> [Name, Label, [Name, Label,...]] +[<strong>-w, --workingdir</strong> dirname] Formula(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Perform elemental analysis using molecular formula(s) specified on the command line.</p> +<p>In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N - +other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O, +8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including +D and T, are not supported.</p> +<p> +</p> +<h2>PARAMETERS</h2> +<dl> +<dt><strong><strong>Formulas</strong> <em>Formula1 [Formula2...]</em></strong></dt> +<dd> +<p><em>Formulas</em> is a space delimited list of molecular formulas to use for elemental analysis.</p> +<p>Input value format is: <em>Formula1 [Formula2 Formula3...]</em>. Default: <em>H2O</em>. +Examples:</p> +<div class="OptionsBox"> + HCl +<br/> HCl, C3H7O2N +<br/> H2O2 Ca3(PO4)2 [PCl4]+</div> +</dd> +</dl> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>--fast</strong></strong></dt> +<dd> +<p>In this mode, the specified formulas are considered valid and initial formula +validation check is skipped.</p> +</dd> +<dt><strong><strong>-m, --mode</strong> <em>All | "ElementalAnalysis,[MolecularWeight,ExactMass]"</em></strong></dt> +<dd> +<p>Specify what values to calculate using molecular formulas specified on command +line: calculate all supported values or specify a comma delimited list of values. Possible +values: <em>All | "ElementalAnalysis, [MolecularWeight, ExactMass]"</em>. Default: <em>All</em>.</p> +</dd> +<dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt> +<dd> +<p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em> +Default value: <em>comma</em>.</p> +</dd> +<dt><strong><strong>--output</strong> <em>STDOUT | File</em></strong></dt> +<dd> +<p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default: +<em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p> +</dd> +<dt><strong><strong>--outputstyle</strong> <em>FormulaBlock | FormulaRows</em></strong></dt> +<dd> +<p>Specify how to list calculated values: add a new line for each property and present it as a block +for each formula; or include all properties in one line and show it as a single line.</p> +<p>Possible values: <em>FormulaBlock | FormulaRows</em>. Default: <em>FormulaBlock</em></p> +<p>An example for <em>FormulaBlock</em> output style:</p> +<div class="OptionsBox"> + Formula: H2O +<br/> ElementalAnalysis: H: H: 11.1898%; O: 88.8102% +<br/> MolecularWeight: 18.0153 +<br/> ExactMass: 18.0106 +<br/> ... ... +<br/> ... ... +<br/> ... ...</div> +<div class="OptionsBox"> + Formula: H2O2 +<br/> ElementalAnalysis: H: 5.9265%; O: 94.0735% +<br/> MolecularWeight: 34.0147 +<br/> ExactMass: 34.0055 +<br/> ... ... +<br/> ... ... +<br/> ... ...</div> +<p>An example for <em>FormulaRows</em> output style:</p> +<div class="OptionsBox"> + Formula,ElementalAnalysis,MolecularWeight,ExactMass +<br/> H2O,H: 11.1898%; O: 88.8102%,18.0153,18.0106 +<br/> H2O2,H: 5.9265%; O: 94.0735%,34.0147,34.0055</div> +</dd> +<dt><strong><strong>-o, --overwrite</strong></strong></dt> +<dd> +<p>Overwrite existing files.</p> +</dd> +<dt><strong><strong>--precision</strong> <em>number</em></strong></dt> +<dd> +<p>Precision for listing numerical values. Default: up to <em>4</em> decimal places. +Valid values: positive integers.</p> +</dd> +<dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> +<dd> +<p>New text file name is generated using the root: <Root>.<Ext>. File name is only +used during <em>File</em> value of <strong>-o, --output</strong> option.</p> +<p>Default file name: FormulsElementalAnalysis.<Ext>. The csv, and tsv +<Ext> values are used for comma/semicolon, and tab delimited text files respectively.</p> +</dd> +<dt><strong><strong>-v --valuelabels</strong> <em>Name,Label,[Name,Label,...]</em></strong></dt> +<dd> +<p>Specify labels to use for calculated values. In general, it's a comma delimited +list of value name and column label pairs. Supported value names: <em>ElementalAnalysis, +MolecularWeight, and ExactMass</em>. Default labels: <em>ElementalAnalysis, MolecularWeight, +and ExactMass</em>.</p> +</dd> +<dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> +<dd> +<p>Location of working directory. Default: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>To perform elemental analysis, calculate molecular weight and exact mass for H2O, +type:</p> +<div class="ExampleBox"> + % ElementalAnalysis.pl</div> +<p>To perform elemental analysis, calculate molecular weight and exact mass for +Ca3(PO4)2 and [PCl4]+, type:</p> +<div class="ExampleBox"> + % ElementalAnalysis.pl "Ca3(PO4)2" "[PCl4]+"</div> +<p>To perform elemental analysis, use label analysis for calculated data, and generate a +new CSV file ElementalAnalysis.csv for H2O and H2O2, type:</p> +<div class="ExampleBox"> + % ElementalAnalysis.pl --m ElementalAnalysis --output File + --valuelabels "ElementalAnalysis,Analysis" -o -r ElementalAnalysis.csv + H2O H2O2</div> +<p>To calculate molecular weight and exact mass with four decimal precision and +generate a new CSV file WeightAndMass.csv with data rows for H2O and H2O2, type:</p> +<div class="ExampleBox"> + % ElementalAnalysis.pl --m "MolecularWeight,ExactMass" --output File + --outputstyle FormulaRows -o -r WeightAndMass.csv + H2O H2O2</div> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./ElementalAnalysisSDFiles.html">ElementalAnalysisSDFiles.pl</a>, <a href="./ElementalAnalysisTextFiles.html">ElementalAnalysisTextFiles.pl</a> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./DBTablesToTextFiles.html" title="DBTablesToTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ElementalAnalysisSDFiles.html" title="ElementalAnalysisSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ElementalAnalysis.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>